Schema for LTRharvest - LTR Fragments Identified by LTRharvest

Database: DobsGB1 Primary Table: ltrdigest_LTR Row Count: 854 Data last updated: 2022-10-20

field	example	SQL type	info
`bin`	589	`smallint(5) unsigned`	range
`chrom`	BDQP01000001	`varchar(255)`	values
`chromStart`	527009	`int(10) unsigned`	range
`chromEnd`	534832	`int(10) unsigned`	range
`name`	LTR_retrotransposon1_LTR	`varchar(255)`	values
`score`	1000	`int(10) unsigned`	range
`strand`	-	`char(1)`	values
`thickStart`	527009	`int(10) unsigned`	range
`thickEnd`	534832	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	2	`int(10) unsigned`	range
`blockSizes`	509,525	`longblob`
`chromStarts`	0,7298	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	score	strand	thickStart	thickEnd	blockCount	blockSizes	chromStarts
589	BDQP01000001	527009	534832	LTR_retrotransposon1_LTR	1000	-	527009	534832	2	509,525	0,7298
597	BDQP01000001	1613894	1623102	LTR_retrotransposon2_LTR	1000	+	1613894	1623102	2	1765,1768	0,7440
592	BDQP01000002	1022796	1024813	LTR_retrotransposon3_LTR	1000	-	1022796	1024813	2	611,614	0,1403
585	BDQP01000003	14341	22513	LTR_retrotransposon4_LTR	1000	-	14341	22513	2	185,177	0,7995
585	BDQP01000003	28107	41438	LTR_retrotransposon5_LTR	1000	+	28107	41438	2	231,234	0,13097
585	BDQP01000003	41596	47504	LTR_retrotransposon6_LTR	1000	-	41596	47504	2	1860,1861	0,4047
606	BDQP01000003	2786785	2793195	LTR_retrotransposon7_LTR	1000	+	2786785	2793195	2	319,314	0,6096
595	BDQP01000004	1319597	1325894	LTR_retrotransposon8_LTR	1000	-	1319597	1325894	2	288,286	0,6011
602	BDQP01000004	2301565	2303583	LTR_retrotransposon9_LTR	1000	-	2301565	2303583	2	82,98	0,1920
605	BDQP01000004	2688823	2696218	LTR_retrotransposon10_LTR	1000	-	2688823	2696218	2	589,593	0,6802

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

LTRharvest (ltrdigest) Track Description


	Description LTRharvest is used to identify putative long terminal repeats (LTR) retrotransposons in the D. obscura genome using the following parameters: `-seed 76 -minlenltr 116 -maxlenltr 800 -mindistltr 2280 -maxdistltr 8773 -similar 91 -xdrop 7 -mat 2 -mis -2 -ins -3 -del -3 -mintsd 4 -maxtsd 20 -vic 60 -overlaps best` Additional features within the LTR retrotransposons are annotated by LTRdigest with the following parameters: `-pptradius 30 -pptlen 8 30 -pptrprob 0.97 -uboxlen 3 30 -pptuprob 0.91 -pbsradius 30 -pbsalilen 11 30 -pbsoffset 0 5 -pbstrnaoffset 0 40 -pbsmaxedist 1 -pbsmatchscore 5 -pbsmismatchscore -10 -pbsinsertionscore -20 -pbsdeletionscore -20 -pdomevalcutoff 1e-6 -maxgaplen 50` The subset of candidates that show significant similarity to Pfam protein domains within LTR retrotransposons are selected and then clustered using the ltrclustering program with the following parameters: `-psmall 80 -plarge 30` References Ellinghaus D, Kurtz S, and Willhoeft U. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics, 9:18, 2008. Steinbiss S, Willhoeft U, Gremme G, and Kurtz S. Fine-grained annotation and classification of de novo predicted LTR retrotransposons. Nucleic Acids Research, 37(21):7002-7013 (2009). Steinbiss S, Kastens S, and Kurtz S. LTRsift: a graphical user interface for semi-automatic classification and postprocessing of de novo detected LTR retrotransposons. Mob DNA. 2012 Nov 7;3(1):18.

Description

References